7BL5 image
Deposition Date 2021-01-18
Release Date 2021-05-12
Last Version Date 2025-04-09
Entry Detail
PDB ID:
7BL5
Keywords:
RIBOSOME
Title:
pre-50S-ObgE particle
Biological Source:
Source Organism:
Escherichia coli str. K-12 substr. MG1655 (Taxon ID: 511145)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7BL5 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:S (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7N4 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:T (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7N9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:U (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7P5 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal silencing factor RsfS
Gene (Uniprot):rsfS
Chain IDs:Z (auth: 6)
Chain Length:105
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0AAT6 Pfam ID:PF02410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal large subunit pseudouridine synthase D
Gene (Uniprot):rluD
Chain IDs:AA (auth: 7)
Chain Length:326
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P33643 Pfam ID:PF01479, PF00849 EC:5.4.99.23
Protein Blast
Polymer Type:polypeptide(L)
Molecule:UPF0307 protein YjgA
Gene (Uniprot):darP
Chain IDs:BA (auth: 8)
Chain Length:183
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A8X0 Pfam ID:PF04751
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTPase ObgE/CgtA
Gene (Uniprot):obgE
Chain IDs:CA (auth: 9)
Chain Length:390
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P42641 Pfam ID:PF01018, PF01926
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:EA (auth: A)
Chain Length:2919
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:V (auth: B)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:A (auth: C)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:B (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:C (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P60723 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:HA (auth: F)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:D (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0AG55 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:W (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:E (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:X (auth: K)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0ADY3 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:F (auth: L)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:DA (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:G (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0AG44 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:H (auth: O)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0C018 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:Y (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7K6 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:I (auth: Q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7L3 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:J (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0AG48 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:K (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P61175 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:L (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0ADZ0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:M (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:N (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:O (auth: W)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7L8 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:P (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7M2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:Q (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7M6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:R (auth: Z)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0AG51 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:IA (auth: b)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7M9 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:GA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli str. K-12 substr. MG1655
UniProt ID:P0A7J3 Pfam ID:PF00466
Ligand Molecules
GDP
MG
ZN
Primary Citation
Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization.
Mol.Cell 81 1200 1215.e9 (2021)
PMID: 33639093 DOI: 10.1016/j.molcel.2021.02.006

Abstact

Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes.

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Disease

Primary Citation of related structures
7BL5